Runs of homozygosity (ROH) are identified in four dairy cattle breeds using NGS data. Cattle populations have been exposed to strong artificial selection for some generations. Genomic regions under selection will show increased levels of ROH. By investigating the relationship between ROH and distribution of predicted deleterious and tolerated variants, we can gain insight into how selection shapes the distribution of functional variants in inbred regions. We observe that predicted deleterious variants are more enriched in ROHs than predicted tolerated variants. Moreover, increase of enrichment of deleterious variants is significantly more pronounced in short and medium ROH regions than long ROH regions (p<0.001). This study demonstrates that artificial selection strongly shapes the distribution of functional variants in ROH regions in cattle populations and contributes in understanding the effects of inbreeding on shaping the distribution of functional variants in cattle genome